Brown University

About: Brown University is a education organization based out in Providence, Rhode Island, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 35778 authors who have published 90896 publications receiving 4471489 citations. The organization is also known as: brown.edu & Brown.

Removing technical variability in RNA-seq data using conditional quantile normalization

Abstract: The ability to measure gene expression on a genome-wide scale is one of the most promising accomplishments in molecular biology. Microarrays, the technology that first permitted this, were riddled with problems due to unwanted sources of variability. Many of these problems are now mitigated, after a decade's worth of statistical methodology development. The recently developed RNA sequencing (RNA-seq) technology has generated much excitement in part due to claims of reduced variability in comparison to microarrays. However, we show that RNA-seq data demonstrate unwanted and obscuring variability similar to what was first observed in microarrays. In particular, we find guanine-cytosine content (GC-content) has a strong sample-specific effect on gene expression measurements that, if left uncorrected, leads to false positives in downstream results. We also report on commonly observed data distortions that demonstrate the need for data normalization. Here, we describe a statistical methodology that improves precision by 42% without loss of accuracy. Our resulting conditional quantile normalization algorithm combines robust generalized regression to remove systematic bias introduced by deterministic features such as GC-content and quantile normalization to correct for global distortions.

Missing Women and the Price of Tea in China: The Effect of Sex-Specific Earnings on Sex Imbalance

Abstract: Economists have long argued that the sex imbalance in developing countries is caused by underlying economic conditions. This paper uses exogenous increases in sex-specific agricultural income caused by post-Mao reforms in China to estimate the effects of total income and sex-specific income on sex-differential survival of children. Increasing female income, holding male income constant, improves survival rates for girls, whereas increasing male income, holding female income constant, worsens survival rates for girls. Increasing female income increases educational attainment of all children, whereas increasing male income decreases educational attainment for girls and has no effect on boys' educational attainment.

Direction of self-motion is perceived from optical flow

Abstract: Can moving observers distinguish the direction in which they are moving from the direction in which they are looking? Radial patterns of optical flow could be used to perceive the translational direction of self-motion and to guide locomotion. However, these patterns are confounded by eye movements, which has led previous investigators to reject the outflow pattern and to propose alternative strategies. Using computer-generated displays of optical flow, we show here that humans can perceive their direction of self-motion during stationary fixations, pursuit eye movements, and with displays that simulate the effects of eye movements. We conclude that optical flow is sufficient for perceiving the direction of self-motion and provide evidence for a theory based on differential element motion.

Internalization of ionotropic glutamate receptors in response to mGluR activation.

Abstract: Activation of group 1 metabotropic glutamate receptors (mGluRs) stimulates dendritic protein synthesis and long-term synaptic depression (LTD), but it remains unclear how these effects are related. Here we provide evidence that a consequence of mGluR activation in the hippocampus is the rapid loss of both AMPA and NMDA receptors from synapses. Like mGluR-LTD, the stable expression of this change requires protein synthesis. These data suggest that expression of mGluR-LTD is at least partly postsynaptic, and that a functional consequence of dendritic protein synthesis is the regulation of glutamate receptor trafficking.

Internal Structure and Early Thermal Evolution of Mars from Mars Global Surveyor Topography and Gravity

Abstract: Topography and gravity measured by the Mars Global Surveyor have enabled determination of the global crust and upper mantle structure of Mars. The planet displays two distinct crustal zones that do not correlate globally with the geologic dichotomy: a region of crust that thins progressively from south to north and encompasses much of the southern highlands and Tharsis province and a region of approximately uniform crustal thickness that includes the northern lowlands and Arabia Terra. The strength of the lithosphere beneath the ancient southern highlands suggests that the northern hemisphere was a locus of high heat flow early in martian history. The thickness of the elastic lithosphere increases with time of loading in the northern plains and Tharsis. The northern lowlands contain structures interpreted as large buried channels that are consistent with northward transport of water and sediment to the lowlands before the end of northern hemisphere resurfacing.